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- PDB-2br4: cmcI-D160 Mg-SAM -

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Basic information

Entry
Database: PDB / ID: 2br4
TitlecmcI-D160 Mg-SAM
ComponentsCEPHALOSPORIN HYDROXYLASE CMCI
KeywordsPORIN / CEPHAMYCIN BIOSYNTHESIS
Function / homology
Function and homology information


lipid biosynthetic process / methyltransferase activity
Similarity search - Function
Rhamnosyl O-methyltransferase/Cephalosporin hydroxylase / Rhamnosyl O-methyltransferase/CmcI / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / Cephalosporin hydroxylase CmcI / Cephalosporin hydroxylase CmcI
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsOster, L.M. / Lester, D.R. / Terwisscha van Scheltinga, A. / Svenda, M. / Genereux, C. / Andersson, I.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Insights Into Cephamycin Biosynthesis: The Crystal Structure of Cmci from Streptomyces Clavuligerus.
Authors: Oster, L.M. / Lester, D.R. / Terwisscha Van Scheltinga, A. / Svenda, M. / Van Lun, M. / Genereux, C. / Andersson, I.
History
DepositionMay 1, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CEPHALOSPORIN HYDROXYLASE CMCI
B: CEPHALOSPORIN HYDROXYLASE CMCI
C: CEPHALOSPORIN HYDROXYLASE CMCI
D: CEPHALOSPORIN HYDROXYLASE CMCI
E: CEPHALOSPORIN HYDROXYLASE CMCI
F: CEPHALOSPORIN HYDROXYLASE CMCI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,71724
Polymers165,8906
Non-polymers3,82818
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.541, 102.364, 181.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
CEPHALOSPORIN HYDROXYLASE CMCI / CMCI


Mass: 27648.264 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O85726, UniProt: B5GLB3*PLUS

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Non-polymers , 5 types, 333 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O8
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN B, LEU 200 TO PHE ...ENGINEERED RESIDUE IN CHAIN A, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN B, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN C, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN D, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN E, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN F, LEU 200 TO PHE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.2 M1reservoirMgCl2
20.1 MTris1reservoirpH7.5
310-14 %PEG40001reservoir
44-7 %PEG10001reservoir
510 mMSAM1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→51.3 Å / Num. obs: 53933 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 51.3 Å / Redundancy: 7 % / Num. measured all: 876420 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BM8

2bm8


Resolution: 2.59→51.3 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.884 / SU B: 10.807 / SU ML: 0.23 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.081 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2701 5 %RANDOM
Rwork0.199 ---
obs0.202 51166 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.59→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11461 0 254 315 12030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02112090
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210624
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9616418
X-RAY DIFFRACTIONr_angle_other_deg0.908324585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96951383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.21690
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213398
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022661
X-RAY DIFFRACTIONr_nbd_refined0.1980.22413
X-RAY DIFFRACTIONr_nbd_other0.2240.212368
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.27027
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.511.56976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.945211243
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.93235114
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6214.55175
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.65 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.36 173
Rwork0.276 3570
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.58980.37070.12891.60050.08310.4965-0.0607-0.06630.0479-0.03630.0536-0.2411-0.00960.11960.00710.01320.01610.01580.0918-0.02980.119741.22156.035343.9664
20.58860.05880.01710.81740.1730.6521-0.03670.02760.018-0.12970.04260.02490.0548-0.0246-0.00590.04170.0193-0.00290.0527-0.02060.049121.471341.352131.8602
30.5648-0.2856-0.47460.97010.17290.39270.02210.0429-0.0375-0.0096-0.00920.0628-0.0176-0.0134-0.01290.0349-0.0318-0.04460.0878-0.02250.1248-7.526742.594645.651
40.62590.1209-0.23790.8624-0.06770.882-0.02880.0138-0.0724-0.01930.0710.03210.0903-0.1227-0.04220.1614-0.0309-0.02340.15130.00580.053715.498258.213987.4917
50.52680.3615-0.30140.2789-0.18021.2219-0.1035-0.0492-0.12360.03480.0563-0.17310.20010.21960.04720.17980.0045-0.0440.1703-0.02520.134240.32756.00275.9587
60.51250.10030.16971.08310.1780.58990.0371-0.2276-0.06790.2813-0.03690.10270.2037-0.1247-0.00020.163-0.05310.03530.2230.02450.1536-7.876441.700273.1528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 230
2X-RAY DIFFRACTION2B4 - 230
3X-RAY DIFFRACTION3C4 - 230
4X-RAY DIFFRACTION4D4 - 230
5X-RAY DIFFRACTION5E4 - 230
6X-RAY DIFFRACTION6F4 - 230
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 51.3 Å / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.14
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.69 Å

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